The present application generally relates to optimization-based control methods, systems and apparatus for internal combustion engines including an air handling system, and more particularly to controlling air handling system actuators in such systems. In certain engine operating conditions, desired emission limits can be violated due to transients, disturbances, and/or other variations in the engine system. Existing approaches in maintaining desired emissions limits do not provide adequate air handling control responses to these operating conditions and suffer from a number of limitations and shortcomings. Therefore, a need remains for further improvements in systems, apparatus, and methods for controlling air handling systems.